NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q02988 UniProt NPD GO	LECA_PLEWA	Lectin precursor	0.03	-	cyt	0	Secreted protein. Secreted into the inner layer of egg jelly				172
Q588G0 UniProt NPD GO	LEP_FUGRU	Leptin precursor	0.03	-	nuc	1 *	Secreted protein (Probable)				152
P30184 UniProt NPD GO	AMPL1_ARATH	Leucine aminopeptidase 1 (EC 3.4.11.1) (LAP 1) (Leucyl aminopeptidase 1) (Proline aminopeptidase 1) ...	0.03	-	cyt	0	Cytoplasm				520
P51092 UniProt NPD GO	LDOX_PETHY	Leucoanthocyanidin dioxygenase (EC 1.14.11.19) (LDOX) (Leucocyanidin oxygenase) (Leucoanthocyanidin ...	0.03	-	cyt	0					430
P67802 UniProt NPD GO	LSK2_LEUMA	Leucosulfakinin-2 (Leucosulfakinin-II) (LSK-II)	0.03	-		0					10
P67803 UniProt NPD GO	LSK2_PERAM	Leucosulfakinin-2 (Leucosulfakinin-II) (LSK-II)	0.03	-		0					10
P80736 UniProt NPD GO	CPI2_PIG	Leukocyte cysteine proteinase inhibitor 2 (PLCPII) (Stefin D2) (Fragment)	0.03	-	nuc	0	Cytoplasm				35
Q60860 UniProt NPD GO	LTC4S_MOUSE	Leukotriene C4 synthase (EC 4.4.1.20) (Leukotriene-C(4) synthase) (LTC4 synthase)	0.03	-	end	3 *	Membrane; multi-pass membrane protein				150
Q85A82 UniProt NPD GO	CHLL_ANTFO	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.03	-	nuc	0	Plastid; chloroplast				290
Q6YXQ7 UniProt NPD GO	CHLL_PHYPA	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.03	-	nuc	0	Plastid; chloroplast				295
P26181 UniProt NPD GO	CHLL_PINCO	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.03	-	nuc	0	Plastid; chloroplast				291
P37843 UniProt NPD GO	CHLB_ARAHE	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.03	-	mit	0	Plastid; chloroplast				103
Q32214 UniProt NPD GO	CHLB_EQUSC	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.03	-	cyt	0	Plastid; chloroplast				103
P54857 UniProt NPD GO	TGL2_YEAST	Lipase 2 (EC 3.1.1.3) (Triacylglycerol lipase)	0.03	-	cyt	0					326
Q9P8W5 UniProt NPD GO	LIP2_CANAL	Lipase 2 precursor (EC 3.1.1.3)	0.03	-	exc	0	Secreted protein				466
Q9P4E6 UniProt NPD GO	LIP9_CANAL	Lipase 9 precursor (EC 3.1.1.3)	0.03	-	mit	0	Secreted protein				453
Q9ZU49 UniProt NPD GO	LPP1_ARATH	Lipid phosphate phosphatase 1 (EC 3.1.3.-) (AtLPP1) (Phosphatidic acid phosphatase 1) (AtPAP1) (Pren ...	0.03	-	end	6	Membrane; multi-pass membrane protein (Probable)				327
Q61469 UniProt NPD GO	LPP1_MOUSE	Lipid phosphate phosphohydrolase 1 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2a) (Phosphatidate ph ...	0.03	-	end	6 *	Cell membrane; multi-pass membrane protein. Found predominantly in plasma membrane	integral to plasma membrane [TAS] membrane fraction [ISS] plasma membrane [TAS]			283
Q8BGA2 UniProt NPD GO	LHPL2_MOUSE	Lipoma HMGIC fusion partner-like 2 protein	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				222
Q9JLJ0 UniProt NPD GO	LITAF_MOUSE	Lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog (LPS-induced TNF-alpha factor ...	0.03	-	nuc	0	Lysosome; lysosomal membrane; peripheral membrane protein; cytoplasmic side (By similarity). Associa ...				161
Q6NZH4 UniProt NPD GO	LIS1_XENTR	Lissencephaly-1 homolog	0.03	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Localizes to the plus end of microtubules and ...				409
Q9PTR5 UniProt NPD GO	LIS1_CHICK	Lissencephaly-1 homolog (LIS-1) (chLIS1)	0.03	-	cyt	0	Cytoplasm (By similarity). Localizes to the plus ends of microtubules and to the centrosome (By simi ...				409
Q6DE72 UniProt NPD GO	LIS1A_XENLA	Lissencephaly-1 homolog A	0.03	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Localizes to the plus end of microtubules and ...				409
Q803D2 UniProt NPD GO	LIS1B_BRARE	Lissencephaly-1 homolog B	0.03	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Localizes to the plus end of microtubules and ...				409
Q64419 UniProt NPD GO	EST1_MESAU	Liver carboxylesterase precursor (EC 3.1.1.1)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomal membrane, lumen of endoplasmic reticu ...				561
P16339 UniProt NPD GO	DNF1_LOCMI	Locupressin (Diuretic neuropeptide F1/F2)	0.03	-		0	Secreted protein				9
P20404 UniProt NPD GO	LPK1_LOCMI	Locustapyrokinin-1 (Lom-PK-1)	0.03	-		0	Secreted protein				16
P01379 UniProt NPD GO	NXL1_LATSE	Long neurotoxin 1 precursor (Neurotoxin alpha) (Component LSIII)	0.03	-	nuc	0	Secreted protein			1LSI	87
P01395 UniProt NPD GO	NXL2_DENVI	Long neurotoxin 2 (Toxin I/V)	0.03	-	nuc	0	Secreted protein				73
O42257 UniProt NPD GO	NXL7_NAJSP	Long neurotoxin 7 precursor	0.03	-	nuc	1 *	Secreted protein				90
Q8SPF8 UniProt NPD GO	LPLC1_BOVIN	Long palate, lung and nasal epithelium carcinoma-associated protein 1 precursor (Von Ebner minor sal ...	0.03	-	end	1 *	Secreted protein (By similarity)				473
P59826 UniProt NPD GO	LPLC3_HUMAN	Long palate, lung and nasal epithelium carcinoma-associated protein 3 precursor (Ligand-binding prot ...	0.03	-	end	0	Secreted protein (By similarity). Ref.1: Cytoplasm	cytoplasm [IDA]			476
P53393 UniProt NPD GO	SUT3_STYHA	Low affinity sulfate transporter 3	0.03	-	end	9	Membrane; multi-pass membrane protein (Potential)				644
P52569 UniProt NPD GO	CTR2_HUMAN	Low-affinity cationic amino acid transporter 2 (CAT-2) (CAT2)	0.03	-	end	14 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	601872		658
P82735 UniProt NPD GO	LCR21_ARATH	Low-molecular-weight cysteine-rich protein LCR21 precursor	0.03	-	mit	1 *					82
Q8LFM0 UniProt NPD GO	LCR24_ARATH	Low-molecular-weight cysteine-rich protein LCR24 precursor	0.03	-	exc	1 *					76
Q01158 UniProt NPD GO	LUCI_LUCLA	Luciferin 4-monooxygenase (EC 1.13.12.7) (Luciferase)	0.03	-	nuc	0	Peroxisome (By similarity)				548
Q9BZG9 UniProt NPD GO	LYNX1_HUMAN	Ly-6/neurotoxin-like protein 1 precursor	0.03	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)		606110	1VYE	116
Q9WVC2 UniProt NPD GO	LYNX1_MOUSE	Ly-6/neurotoxin-like protein 1 precursor (GC26)	0.03	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)	membrane fraction [IDA] plasma membrane [IDA]			116
Q9TSV8 UniProt NPD GO	TNFC_PIG	Lymphotoxin-beta (LT-beta) (Tumor necrosis factor C) (TNF-C) (Tumor necrosis factor ligand superfami ...	0.03	-	cyt	0	Membrane; single-pass type II membrane protein (By similarity)				150
P41929 UniProt NPD GO	LYC1_YARLI	Lysine acetyltransferase (EC 2.3.1.32) (Lysine 6-N-acetyltransferase) (LAT)	0.03	-	cyt	0					392
Q1JQA0 UniProt NPD GO	PPT2_BOVIN	Lysosomal thioesterase PPT2 precursor (EC 3.1.2.-) (PPT-2)	0.03	-	nuc	1 *	Lysosome (By similarity)				305
O70489 UniProt NPD GO	PPT2_RAT	Lysosomal thioesterase PPT2 precursor (EC 3.1.2.-) (PPT-2)	0.03	-	exc	0	Lysosome (By similarity)				302
P49130 UniProt NPD GO	LAMP2_CRIGR	Lysosome-associated membrane glycoprotein 2 precursor (LAMP-2) (Lysosomal membrane glycoprotein B) ( ...	0.03	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Endosome; endosomal membrane; si ...				410
P37715 UniProt NPD GO	LYS_ASTRU	Lysozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase) (Fragment)	0.03	-	nuc	0					25
P11941 UniProt NPD GO	LYSC2_ONCMY	Lysozyme C II precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C) (Lysozyme type II)	0.03	-	exc	0				1LMQ	144
P79158 UniProt NPD GO	LYSC_CALJA	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.03	-	vac	0					148
P00701 UniProt NPD GO	LYSC_COTJA	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.03	-	end	0				2IHL	147
Q659U5 UniProt NPD GO	LYSC_HALGR	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.03	-	exc	0					148
P79806 UniProt NPD GO	LYSC_MIOTA	Lysozyme C precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.03	-	vac	0					148

You are viewing entries 80451 to 80500 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.